Bacterial variations on the methionine salvage pathway.

BACKGROUND: The thiomethyl group of S-adenosylmethionine is often recycled as methionine from methylthioadenosine. The corresponding pathway has been unravelled in Bacillus subtilis. However methylthioadenosine is subjected to alternative degradative pathways depending on the organism. RESULTS: This work uses genome in silico analysis to propose methionine salvage pathways for Klebsiella pneumoniae, Leptospira interrogans, Thermoanaerobacter tengcongensis and Xylella fastidiosa. Experiments performed with mutants of B. subtilis and Pseudomonas aeruginosa substantiate the hypotheses proposed. The enzymes that catalyze the reactions are recruited from a variety of origins. The first, ubiquitous, enzyme of the pathway, MtnA (methylthioribose-1-phosphate isomerase), belongs to a family of proteins related to eukaryotic intiation factor 2B alpha. mtnB codes for a methylthioribulose-1-phosphate dehydratase. Two reactions follow, that of an enolase and that of a phosphatase. While in B. subtilis this is performed by two distinct polypeptides, in the other organisms analyzed here an enolase-phosphatase yields 1,2-dihydroxy-3-keto-5-methylthiopentene. In the presence of dioxygen an aci-reductone dioxygenase yields the immediate precursor of methionine, ketomethylthiobutyrate. Under some conditions this enzyme produces carbon monoxide in B. subtilis, suggesting a route for a new gaseous mediator in bacteria. Ketomethylthiobutyrate is finally transaminated by an aminotransferase that exists usually as a broad specificity enzyme (often able to transaminate aromatic aminoacid keto-acid precursors or histidinol-phosphate). CONCLUSION: A functional methionine salvage pathway was experimentally demonstrated, for the first time, in P. aeruginosa. Apparently, methionine salvage pathways are frequent in Bacteria (and in Eukarya), with recruitment of different polypeptides to perform the needed reactions (an ancestor of a translation initiation factor and RuBisCO, as an enolase, in some Firmicutes). Many are highly dependent on the presence of oxygen, suggesting that the ecological niche may play an important role for the existence and/or metabolic steps of the pathway, even in phylogenetically related bacteria. Further work is needed to uncover the corresponding steps when dioxygen is scarce or absent (this is important to explore the presence of the pathway in Archaea). The thermophile T. tengcongensis, that thrives in the absence of oxygen, appears to possess the pathway. It will be an interesting link to uncover the missing reactions in anaerobic environments.

Fibronectin in the area opaca of the young chick embryo. Immunofluorescence and immuno-electron-microscopic study

Distribution of fibronectin-like immunoreactivity was studied in the area opaca of the young chick embryo (stages 4-6 HH) by use of the immunofluorescence and protein A-coupled to colloidal gold techniques. Fibronectin, associated to the basement membrane, formed a fibrillar network, the pattern of which changed from the centre to the periphery of the area opaca. At the ultrastructural level, differences in fibronectin distribution were found between non-moving and moving cells. The epithelial-like cells presented fibronectin staining exclusively on their basal side. Actively migrating cells (edge and mesodermal cells) showed immunoreactive material localized around their entire surface and within the cytoplasm. The fibronectin distribution is discussed in relation to three important phenomena taking place during the early growth of the area opaca: anchorage and migration of the edge cells, modification of cell shape in relation to mechanical tension, and expansion of the area vasculosa.

Taking the fungal highway: mobilization of pollutant-degrading bacteria by fungi.

The capacity of fungi to serve as vectors for the dispersion of pollutant-degrading bacteria was analyzed in laboratory model systems mimicking water-saturated (agar surfaces) and unsaturated soil environments (glass-bead-filled columns). Two common soil fungi (Fusarium oxysporum and Rhexocercosporidium sp.) forming hydrophilic and hydrophobic mycelia, respectively, and three polycyclic aromatic hydrocarbon degrading bacteria (Achromobacter sp. SK1, Mycobacterium frederiksbergense LB501TG, and Sphingomonas sp. L138) were selected based on the absence of mutual antagonistic effects. It was shown that fungal hyphae act as vectors for bacterial transport with mobilization strongly depending on the specific microorganisms chosen: The motile strain Achromobacter sp. SK1 was most efficiently spread along hyphae of hydrophilic F. oxysporum in both model systems with transport velocities of up to 1 cm d(-1), whereas no dispersion of the two nonmotile strains was observed in the presence of F. oxysporum. By contrast, none of the bacteria was mobilized along the hydrophobic mycelia of Rhexocercosporidium sp. growing on agar surfaces. In column experiments however, strain SK1 was mobilized by Rhexocercosporidium sp. It is hypothesized that bacteria may move by their intrinsic motilitythrough continuous (physiological) liquid films forming around fungal hyphae. The results of this study suggest that the specific stimulation of indigenous fungi may be a strategy to mobilize pollutant-degrading bacteria leading to their homogenization in polluted soil thereby improving bioremediation.

Medical record search engines, using pseudonymised patient identity: an alternative to centralised medical records

Purpose The purpose of our multidisciplinary study was to define a pragmatic and secure alternative to the creation of a national centralised medical record which could gather together the different parts of the medical record of a patient scattered in the different hospitals where he was hospitalised without any risk of breaching confidentiality. Methods We first analyse the reasons for the failure and the dangers of centralisation (i.e. difficulty to define a European patients' identifier, to reach a common standard for the contents of the medical record, for data protection) and then propose an alternative that uses the existing available data on the basis that setting up a safe though imperfect system could be better than continuing a quest for a mythical perfect information system that we have still not found after a search that has lasted two decades. Results We describe the functioning of Medical Record Search Engines (MRSEs), using pseudonymisation of patients' identity. The MRSE will be able to retrieve and to provide upon an MD's request all the available information concerning a patient who has been hospitalised in different hospitals without ever having access to the patient's identity. The drawback of this system is that the medical practitioner then has to read all of the information and to create his own synthesis and eventually to reject extra data. Conclusions Faced with the difficulties and the risks of setting up a centralised medical record system, a system that gathers all of the available information concerning a patient could be of great interest. This low-cost pragmatic alternative which could be developed quickly should be taken into consideration by health authorities.

Cryo-electron microscopy of vitreous sections of native biological cells and tissues : methodology and applications

Résumé L'eau est souvent considérée comme une substance ordinaire puisque elle est très commune dans la nature. En fait elle est la plus remarquable de toutes les substances. Sans l'eau la vie sur la terre n'existerait pas. L'eau représente le composant majeur de la cellule vivante, formant typiquement 70 à 95% de la masse cellulaire et elle fournit un environnement à d'innombrables organismes puisque elle couvre 75% de la surface de terre. L'eau est une molécule simple faite de deux atomes d'hydrogène et un atome d'oxygène. Sa petite taille semble en contradiction avec la subtilité de ses propriétés physiques et chimiques. Parmi celles-là, le fait que, au point triple, l'eau liquide est plus dense que la glace est particulièrement remarquable. Malgré son importance particulière dans les sciences de la vie, l'eau est systématiquement éliminée des spécimens biologiques examinés par la microscopie électronique. La raison en est que le haut vide du microscope électronique exige que le spécimen biologique soit solide. Pendant 50 ans la science de la microscopie électronique a adressé ce problème résultant en ce moment en des nombreuses techniques de préparation dont l'usage est courrant. Typiquement ces techniques consistent à fixer l'échantillon (chimiquement ou par congélation), remplacer son contenu d'eau par un plastique doux qui est transformé à un bloc rigide par polymérisation. Le bloc du spécimen est coupé en sections minces (d’environ 50 nm) avec un ultramicrotome à température ambiante. En général, ces techniques introduisent plusieurs artefacts, principalement dû à l'enlèvement d'eau. Afin d'éviter ces artefacts, le spécimen peut être congelé, coupé et observé à basse température. Cependant, l'eau liquide cristallise lors de la congélation, résultant en une importante détérioration. Idéalement, l'eau liquide est solidifiée dans un état vitreux. La vitrification consiste à refroidir l'eau si rapidement que les cristaux de glace n'ont pas de temps de se former. Une percée a eu lieu quand la vitrification d'eau pure a été découverte expérimentalement. Cette découverte a ouvert la voie à la cryo-microscopie des suspensions biologiques en film mince vitrifié. Nous avons travaillé pour étendre la technique aux spécimens épais. Pour ce faire les échantillons biologiques doivent être vitrifiés, cryo-coupées en sections vitreuse et observées dans une cryo-microscope électronique. Cette technique, appelée la cryo- microscopie électronique des sections vitrifiées (CEMOVIS), est maintenant considérée comme étant la meilleure façon de conserver l'ultrastructure de tissus et cellules biologiques dans un état très proche de l'état natif. Récemment, cette technique est devenue une méthode pratique fournissant des résultats excellents. Elle a cependant, des limitations importantes, la plus importante d'entre elles est certainement dû aux artefacts de la coupe. Ces artefacts sont la conséquence de la nature du matériel vitreux et le fait que les sections vitreuses ne peuvent pas flotter sur un liquide comme c'est le cas pour les sections en plastique coupées à température ambiante. Le but de ce travail a été d'améliorer notre compréhension du processus de la coupe et des artefacts de la coupe. Nous avons ainsi trouvé des conditions optimales pour minimiser ou empêcher ces artefacts. Un modèle amélioré du processus de coupe et une redéfinitions des artefacts de coupe sont proposés. Les résultats obtenus sous ces conditions sont présentés et comparés aux résultats obtenus avec les méthodes conventionnelles. Abstract Water is often considered to be an ordinary substance since it is transparent, odourless, tasteless and it is very common in nature. As a matter of fact it can be argued that it is the most remarkable of all substances. Without water life on Earth would not exist. Water is the major component of cells, typically forming 70 to 95% of cellular mass and it provides an environment for innumerable organisms to live in, since it covers 75% of Earth surface. Water is a simple molecule made of two hydrogen atoms and one oxygen atom, H2O. The small size of the molecule stands in contrast with its unique physical and chemical properties. Among those the fact that, at the triple point, liquid water is denser than ice is especially remarkable. Despite its special importance in life science, water is systematically removed from biological specimens investigated by electron microscopy. This is because the high vacuum of the electron microscope requires that the biological specimen is observed in dry conditions. For 50 years the science of electron microscopy has addressed this problem resulting in numerous preparation techniques, presently in routine use. Typically these techniques consist in fixing the sample (chemically or by freezing), replacing its water by plastic which is transformed into rigid block by polymerisation. The block is then cut into thin sections (c. 50 nm) with an ultra-microtome at room temperature. Usually, these techniques introduce several artefacts, most of them due to water removal. In order to avoid these artefacts, the specimen can be frozen, cut and observed at low temperature. However, liquid water crystallizes into ice upon freezing, thus causing severe damage. Ideally, liquid water is solidified into a vitreous state. Vitrification consists in solidifying water so rapidly that ice crystals have no time to form. A breakthrough took place when vitrification of pure water was discovered. Since this discovery, the thin film vitrification method is used with success for the observation of biological suspensions of. small particles. Our work was to extend the method to bulk biological samples that have to be vitrified, cryosectioned into vitreous sections and observed in cryo-electron microscope. This technique is called cryo-electron microscopy of vitreous sections (CEMOVIS). It is now believed to be the best way to preserve the ultrastructure of biological tissues and cells very close to the native state for electron microscopic observation. Since recently, CEMOVIS has become a practical method achieving excellent results. It has, however, some sever limitations, the most important of them certainly being due to cutting artefacts. They are the consequence of the nature of vitreous material and the fact that vitreous sections cannot be floated on a liquid as is the case for plastic sections cut at room temperature. The aim of the present work has been to improve our understanding of the cutting process and of cutting artefacts, thus finding optimal conditions to minimise or prevent these artefacts. An improved model of the cutting process and redefinitions of cutting artefacts are proposed. Results obtained with CEMOVIS under these conditions are presented and compared with results obtained with conventional methods.

Cryo-negative staining: advantages and applications for three-dimensional electron microscopy of biological macromolecules

Les échantillons biologiques ne s?arrangent pas toujours en objets ordonnés (cristaux 2D ou hélices) nécessaires pour la microscopie électronique ni en cristaux 3D parfaitement ordonnés pour la cristallographie rayons X alors que de nombreux spécimens sont tout simplement trop << gros D pour la spectroscopie NMR. C?est pour ces raisons que l?analyse de particules isolées par la cryo-microscopie électronique est devenue une technique de plus en plus importante pour déterminer la structure de macromolécules. Néanmoins, le faible rapport signal-sur-bruit ainsi que la forte sensibilité des échantillons biologiques natifs face au faisceau électronique restent deux parmi les facteurs limitant la résolution. La cryo-coloration négative est une technique récemment développée permettant l?observation des échantillons biologiques avec le microscope électronique. Ils sont observés à l?état vitrifié et à basse température, en présence d?un colorant (molybdate d?ammonium). Les avantages de la cryo-coloration négative sont étudiés dans ce travail. Les résultats obtenus révèlent que les problèmes majeurs peuvent êtres évités par l?utilisation de cette nouvelle technique. Les échantillons sont représentés fidèlement avec un SNR 10 fois plus important que dans le cas des échantillons dans l?eau. De plus, la comparaison de données obtenues après de multiples expositions montre que les dégâts liés au faisceau électronique sont réduits considérablement. D?autre part, les résultats exposés mettent en évidence que la technique est idéale pour l?analyse à haute résolution de macromolécules biologiques. La solution vitrifiée de molybdate d?ammonium entourant l?échantillon n?empêche pas l?accès à la structure interne de la protéine. Finalement, plusieurs exemples d?application démontrent les avantages de cette technique nouvellement développée.<br/><br/>Many biological specimens do not arrange themselves in ordered assemblies (tubular or flat 2D crystals) suitable for electron crystallography, nor in perfectly ordered 3D crystals for X-ray diffraction; many other are simply too large to be approached by NMR spectroscopy. Therefore, single-particles analysis has become a progressively more important technique for structural determination of large isolated macromolecules by cryo-electron microscopy. Nevertheless, the low signal-to-noise ratio and the high electron-beam sensitivity of biological samples remain two main resolution-limiting factors, when the specimens are observed in their native state. Cryo-negative staining is a recently developed technique that allows the study of biological samples with the electron microscope. The samples are observed at low temperature, in the vitrified state, but in presence of a stain (ammonium molybdate). In the present work, the advantages of this novel technique are investigated: it is shown that cryo-negative staining can generally overcome most of the problems encountered with cryo-electron microscopy of vitrified native suspension of biological particles. The specimens are faithfully represented with a 10-times higher SNR than in the case of unstained samples. Beam-damage is found to be considerably reduced by comparison of multiple-exposure series of both stained and unstained samples. The present report also demonstrates that cryo-negative staining is capable of high- resolution analysis of biological macromolecules. The vitrified stain solution surrounding the sample does not forbid the access to the interna1 features (ie. the secondary structure) of a protein. This finding is of direct interest for the structural biologist trying to combine electron microscopy and X-ray data. developed electron microscopy technique. Finally, several application examples demonstrate the advantages of this newly

Investigation of interaction between native and impurity defects in ZnSe

Zinc selenide is a prospective material for optoelectronics. The fabrication of ZnSe­based light-emitting diodes is hindered by complexity of p-type doping of the component materials. The interaction between native and impurity defects, the tendency of doping impurity to form associative centres with native defects and the tendency to self-compensation are the main factors impeding effective control of the value and type of conductivity. The thesis is devoted to the study of the processes of interaction between native and impurity defects in zinc selenide. It is established that the Au impurity has the most prominent amphoteric properties in ZnSe among Cu, Ag and Au impurities, as it forms a great number of both Au; donors and Auz„ acceptors. Electrical measurements show that Ag and Au ions introduced into vacant sites of the Zn sublattice form simple single-charged Agz„+ and Auzn+ states with d1° electron configuration, while Cu ions can form both single-charged Cuz„ (d1) and double-charged Cuzr`+ (d`o) centres. Amphoteric properties of Ag and Au transition metals stimulated by time are found for the first time from both electrical and luminescent measurements. A model that explains the changes in electrical and luminescent parameters by displacement of Ag ions into interstitial sites due to lattice deformation forces is proposed. Formation of an Ag;-donor impurity band in ZnSe samples doped with Ag and stored at room temperature is also studied. Thus, the properties of the doped samples are modified due to large lattice relaxation during aging. This fact should be taken into account in optoelectronic applications of doped ZnSe and related compounds.

Cyclosporine A, an alternative to the oral lichen planus erosive treatment

We present a double-blind study in two groups afflicted with oral lichen planus erythematous of long evolution and resistant to other treatments. We tested on it a treatment with Cyclosporine A (CyA) which had been successfully used before by many dermatologists. In the group A we used mouthwashes with a 5 ml Cyclosporine A solution to a 10% in olive oil of 0.4 degrees of acidity for five minutes, three times a day for eight weeks. In the control group we used acetonide of triamcinolone 01% in aqueous solution. Patients in group A improved considerably in their symptomatology in a 90% against a 60% in group B. In group A we could appreciate a disappearance of the symptomatology after two weeks of treatment in 60% of patients against 30% in group B. CyA can be an alternative to the conventional treatments in the acute period of lichen planus although it can not be considered as a first option drug because of the high cost of the treatment. For long term, results are not so good and we consider that extensive studies are necessary

Neuro-mechanical and metabolic adjustments to the repeated anaerobic sprint test in professional football players.

PURPOSE: This study aimed to determine the neuro-mechanical and metabolic adjustments in the lower limbs induced by the running anaerobic sprint test (the so-called RAST). METHODS: Eight professional football players performed 6 × 35 m sprints interspersed with 10 s of active recovery on artificial turf with their football shoes. Sprinting mechanics (plantar pressure insoles), root mean square activity of the vastus lateralis (VL), rectus femoris (RF), and biceps femoris (BF) muscles (surface electromyography, EMG) and VL muscle oxygenation (near-infrared spectroscopy) were monitored continuously. RESULTS: Sprint time, contact time and total stride duration increased from the first to the last repetition (+17.4, +20.0 and +16.6 %; all P < 0.05), while flight time and stride length remained constant. Stride frequency (-13.9 %; P < 0.001) and vertical stiffness decreased (-27.2 %; P < 0.001) across trials. Root mean square EMG activities of RF and BF (-18.7 and -18.1 %; P < 0.01 and 0.001, respectively), but not VL (-1.2 %; P > 0.05), decreased over sprint repetitions and were correlated with the increase in running time (r = -0.82 and -0.90; both P < 0.05). Together with a better maintenance of RF and BF muscles activation levels over sprint repetitions, players with a better repeated-sprint performance (lower cumulated times) also displayed faster muscle de- (during sprints) and re-oxygenation (during recovery) rates (r = -0.74 and -0.84; P < 0.05 and 0.01, respectively). CONCLUSION: The repeated anaerobic sprint test leads to substantial alterations in stride mechanics and leg-spring behaviour. Our results also strengthen the link between repeated-sprint ability and the change in neuromuscular activation as well as in muscle de- and re-oxygenation rates.

An alternative approach to the prevention of doping in cycling

The article proposes an alternative approach to policies for preventing doping in cycling, based on in-depth analysis of the functioning of nine of the 40 world professional teams and the careers of the 2,351 riders who were or have been professionals since 2005. The first part shows that the instruments of prevention have been based on a questionable understanding of doping as an individual moral fault, and have not produced the expected results. The second part proposes to analyse the ways in which teams and riders produce their achievments, so as to put forward an alternative to the anti-doping policies used hitherto, which have little impact on riders. The study shows that it is more pertinent to examine the forms of employment and the business models, because these have important effects on cycling professionals' conditions of work. It makes it possible to identify three dimensions of the risk of doping on which organisations can act in their antidoping policies: team organisation, riders' preparation and workload, and the precarity of employment.